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Yorodumi- PDB-3ok2: Crystal structure of the ANA:RNA decamer without lattice transloc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ok2 | ||||||
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Title | Crystal structure of the ANA:RNA decamer without lattice translocation defects | ||||||
Components |
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Keywords | RNA / hybrid / ANA / sugar modification / altritol sugar rings | ||||||
Function / homology | OTHER / OTHER (> 10) / RNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.963 Å | ||||||
Authors | Ovaere, M. / Van Meervelt, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex. Authors: Ovaere, M. / Sponer, J. / Sponer, J.E. / Herdewijn, P. / Van Meervelt, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ok2.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ok2.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ok2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/3ok2 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/3ok2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Other | Mass: 3354.144 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Molecule was synthesized #2: RNA chain | Mass: 3216.973 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Molecule was synthesized #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.01M NiCl2, 1.0M Li2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2009 | |||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.96→39.45 Å / Num. all: 11922 / Num. obs: 11922 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.066 / Net I/σ(I): 9.3 | |||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.963→39.45 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 4.726 / SU ML: 0.129 / σ(F): 0 / ESU R: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.963→39.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.963→2.014 Å / Total num. of bins used: 20
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